We use large-scale Monte-Carlo simulations to study thermal fluctuations in chiral $p$-wave superconductors in an applied magnetic field in three dimensions. We consider the thermal stability of previously predicted unusual double-quanta flux-line lattice ground states in such superconductors. In previous works it was shown that, neglecting thermal fluctuations, a chiral $p$-wave superconductor forms a hexagonal lattice of doubly-quantized vortices, except extremely close to the vicinity of $H_{c2}$ where double-quanta vortices split apart. We find dissociation of double-quanta vortices driven by thermal fluctuations. However, our calculations also show that the previous predictions of hexagonal doubly-quantized vortices, where thermal fluctuations were ignored, are very robust in the considered model.